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From Ted Yu <yuzhih...@gmail.com>
Subject Re: Scanner timeouts
Date Fri, 28 Oct 2016 17:36:59 GMT
For your first question, you need to pass hbase-site.xml which has config
parameters affecting client operations to Spark  executors.

bq. missed indexing some column

hbase doesn't have indexing (as in the sense of traditional RDBMS).

Let's see what happens after hbase-site.xml is passed to executors.

BTW Can you tell us the release of hbase you're using ?



On Fri, Oct 28, 2016 at 10:22 AM, Pat Ferrel <pat@occamsmachete.com> wrote:

> So to clarify there are some values in hbase/conf/hbase-site.xml that are
> needed by the calling code in the Spark driver and executors and so must be
> passed using --files to spark-submit? If so I can do this.
>
> But do I have a deeper issue? Is it typical to need a scan like this? Have
> I missed indexing some column maybe?
>
>
> On Oct 28, 2016, at 9:59 AM, Ted Yu <yuzhihong@gmail.com> wrote:
>
> Mich:
> bq. on table 'hbase:meta' *at region=hbase:meta,,1.1588230740
>
> What you observed was different issue.
> The above looks like trouble with locating region(s) during scan.
>
> On Fri, Oct 28, 2016 at 9:54 AM, Mich Talebzadeh <
> mich.talebzadeh@gmail.com>
> wrote:
>
> > This is an example I got
> >
> > warning: there were two deprecation warnings; re-run with -deprecation
> for
> > details
> > rdd1: org.apache.spark.rdd.RDD[(String, String)] = MapPartitionsRDD[77]
> at
> > map at <console>:151
> > defined class columns
> > dfTICKER: org.apache.spark.sql.Dataset[columns] = [KEY: string, TICKER:
> > string]
> > org.apache.hadoop.hbase.client.RetriesExhaustedException: Failed after
> > attempts=36, exceptions:
> > *Fri Oct 28 13:13:46 BST 2016, null, java.net.SocketTimeoutException:
> > callTimeout=60000, callDuration=68411: row
> > 'MARKETDATAHBASE,,00000000000000' on table 'hbase:meta' *at
> > region=hbase:meta,,1.1588230740, hostname=rhes564,16201,1477246132044,
> > seqNum=0
> >  at
> > org.apache.hadoop.hbase.client.RpcRetryingCallerWithReadRepli
> > cas.throwEnrichedException(RpcRetryingCallerWithReadReplicas.java:276)
> >  at
> > org.apache.hadoop.hbase.client.ScannerCallableWithReplicas.call(
> > ScannerCallableWithReplicas.java:210)
> >  at
> > org.apache.hadoop.hbase.client.ScannerCallableWithReplicas.call(
> > ScannerCallableWithReplicas.java:60)
> >  at
> > org.apache.hadoop.hbase.client.RpcRetryingCaller.callWithoutRetries(
> > RpcRetryingCaller.java:210)
> >
> >
> >
> > Dr Mich Talebzadeh
> >
> >
> >
> > LinkedIn * https://www.linkedin.com/profile/view?id=
> > AAEAAAAWh2gBxianrbJd6zP6AcPCCdOABUrV8Pw
> > <https://www.linkedin.com/profile/view?id=AAEAAAAWh2gBxianrbJd6zP6AcPCCd
> > OABUrV8Pw>*
> >
> >
> >
> > http://talebzadehmich.wordpress.com
> >
> >
> > *Disclaimer:* Use it at your own risk. Any and all responsibility for any
> > loss, damage or destruction of data or any other property which may arise
> > from relying on this email's technical content is explicitly disclaimed.
> > The author will in no case be liable for any monetary damages arising
> from
> > such loss, damage or destruction.
> >
> >
> >
> > On 28 October 2016 at 17:52, Pat Ferrel <pat@occamsmachete.com> wrote:
> >
> >> I will check that, but if that is a server startup thing I was not aware
> > I
> >> had to send it to the executors. So it’s like a connection timeout from
> >> executor code?
> >>
> >>
> >> On Oct 28, 2016, at 9:48 AM, Ted Yu <yuzhihong@gmail.com> wrote:
> >>
> >> How did you change the timeout(s) ?
> >>
> >> bq. timeout is currently set to 60000
> >>
> >> Did you pass hbase-site.xml using --files to Spark job ?
> >>
> >> Cheers
> >>
> >> On Fri, Oct 28, 2016 at 9:27 AM, Pat Ferrel <pat@occamsmachete.com>
> > wrote:
> >>
> >>> Using standalone Spark. I don’t recall seeing connection lost errors,
> > but
> >>> there are lots of logs. I’ve set the scanner and RPC timeouts to large
> >>> numbers on the servers.
> >>>
> >>> But I also saw in the logs:
> >>>
> >>>   org.apache.hadoop.hbase.client.ScannerTimeoutException: 381788ms
> >>> passed since the last invocation, timeout is currently set to 60000
> >>>
> >>> Not sure where that is coming from. Does the driver machine making
> >> queries
> >>> need to have the timeout config also?
> >>>
> >>> And why so large, am I doing something wrong?
> >>>
> >>>
> >>> On Oct 28, 2016, at 8:50 AM, Ted Yu <yuzhihong@gmail.com> wrote:
> >>>
> >>> Mich:
> >>> The OutOfOrderScannerNextException indicated problem with read from
> >> hbase.
> >>>
> >>> How did you know connection to Spark cluster was lost ?
> >>>
> >>> Cheers
> >>>
> >>> On Fri, Oct 28, 2016 at 8:47 AM, Mich Talebzadeh <
> >>> mich.talebzadeh@gmail.com>
> >>> wrote:
> >>>
> >>>> Looks like it lost the connection to Spark cluster.
> >>>>
> >>>> What mode you are using with Spark, Standalone, Yarn or others. The
> >> issue
> >>>> looks like a resource manager issue.
> >>>>
> >>>> I have seen this when running Zeppelin with Spark on Hbase.
> >>>>
> >>>> HTH
> >>>>
> >>>> Dr Mich Talebzadeh
> >>>>
> >>>>
> >>>>
> >>>> LinkedIn * https://www.linkedin.com/profile/view?id=
> >>>> AAEAAAAWh2gBxianrbJd6zP6AcPCCdOABUrV8Pw
> >>>> <https://www.linkedin.com/profile/view?id=
> >> AAEAAAAWh2gBxianrbJd6zP6AcPCCd
> >>>> OABUrV8Pw>*
> >>>>
> >>>>
> >>>>
> >>>> http://talebzadehmich.wordpress.com
> >>>>
> >>>>
> >>>> *Disclaimer:* Use it at your own risk. Any and all responsibility for
> >> any
> >>>> loss, damage or destruction of data or any other property which may
> >> arise
> >>>> from relying on this email's technical content is explicitly
> > disclaimed.
> >>>> The author will in no case be liable for any monetary damages arising
> >>> from
> >>>> such loss, damage or destruction.
> >>>>
> >>>>
> >>>>
> >>>> On 28 October 2016 at 16:38, Pat Ferrel <pat@occamsmachete.com>
> > wrote:
> >>>>
> >>>>> I’m getting data from HBase using a large Spark cluster with
> >> parallelism
> >>>>> of near 400. The query fails quire often with the message below.
> >>>> Sometimes
> >>>>> a retry will work and sometimes the ultimate failure results (below).
> >>>>>
> >>>>> If I reduce parallelism in Spark it slows other parts of the
> > algorithm
> >>>>> unacceptably. I have also experimented with very large RPC/Scanner
> >>>> timeouts
> >>>>> of many minutes—to no avail.
> >>>>>
> >>>>> Any clues about what to look for or what may be setup wrong in my
> >>> tables?
> >>>>>
> >>>>> Job aborted due to stage failure: Task 44 in stage 147.0 failed
4
> >> times,
> >>>>> most recent failure: Lost task 44.3 in stage 147.0 (TID 24833,
> >>>>> ip-172-16-3-9.eu-central-1.compute.internal):
> > org.apache.hadoop.hbase.
> >>>> DoNotRetryIOException:
> >>>>> Failed after retry of OutOfOrderScannerNextException: was there
a
> > rpc
> >>>>> timeout?+details
> >>>>> Job aborted due to stage failure: Task 44 in stage 147.0 failed
4
> >> times,
> >>>>> most recent failure: Lost task 44.3 in stage 147.0 (TID 24833,
> >>>>> ip-172-16-3-9.eu-central-1.compute.internal):
> > org.apache.hadoop.hbase.
> >>>> DoNotRetryIOException:
> >>>>> Failed after retry of OutOfOrderScannerNextException: was there
a
> > rpc
> >>>>> timeout? at org.apache.hadoop.hbase.client.ClientScanner.next(
> >>>> ClientScanner.java:403)
> >>>>> at org.apache.hadoop.hbase.mapreduce.TableRecordReaderImpl.
> >>> nextKeyValue(
> >>>>> TableRecordReaderImpl.java:232) at org.apache.hadoop.hbase.
> >>>>> mapreduce.TableRecordReader.nextKeyValue(TableRecordReader.java:138)
> >> at
> >>>>>
> >>>>
> >>>
> >>>
> >>
> >>
> >
>
>

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